As of MediaWiki 1.17 all resources are (or should be) loaded through ResourceLoader. The default modules are stored in /resources. There are no static minified versions anymore as ResourceLoader takes care of this when combining and optimizing all queued files.
All code can assume that jQuery has already been loaded.

However, if your site skin was created prior to 1.17, ResourceLoader will not be loaded and jQuery will not be available.

In 1.16, the jQuery file is in skins/common/jquery.js and the minified version is jquery-min.js in the same directory.

Extensions can use OutputPage's includeJQuery method, which has existed since r61431, to avoid loading minified version of jQuery core multiple times. It should be noted that includeJQuery does not support jQuery plugins and such.